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MBoC  |  PERSPECTIVE

Why should cell biologists study microbial


pathogens?
Matthew D. Welch
Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA 94720

ABSTRACT  One quarter of all deaths worldwide each year result from infectious diseases Monitoring Editor
caused by microbial pathogens. Pathogens infect and cause disease by producing virulence Doug Kellogg
University of California,
factors that target host cell molecules. Studying how virulence factors target host cells has
Santa Cruz
revealed fundamental principles of cell biology. These include important advances in our un-
derstanding of the cytoskeleton, organelles and membrane-trafficking intermediates, signal Received: Jul 15, 2015
transduction pathways, cell cycle regulators, the organelle/protein recycling machinery, and Revised: Aug 12, 2015
cell-death pathways. Such studies have also revealed cellular pathways crucial for the immune Accepted: Aug 14, 2015
response. Discoveries from basic research on the cell biology of pathogenesis are actively
being translated into the development of host-targeted therapies to treat infectious diseas-
es. Thus there are many reasons for cell biologists to incorporate the study of microbial
pathogens into their research programs.

INTRODUCTION
Infectious diseases cause approximately one quarter of all deaths organelle, and then exit the cell to disseminate the infection. They
worldwide each year (Fauci and Morens, 2012). These include the produce virulence factors that promote phagocytosis, enable move-
“big three”—HIV/AIDS, tuberculosis, and malaria—which account ment to their preferred compartment, manipulate membrane traf-
for 10% of all deaths. They also include emerging diseases such as ficking and autophagy to resist killing and permit growth and repli-
Ebola, Middle East Respiratory Syndrome, and methicillin-resistant cation, and exit the cell to promote spread.
Staphylococcus aureus. Infections are caused by microbial patho- The cellular and molecular targets of pathogen virulence factors
gens from different domains of the tree of life—viruses, bacteria, or are the same systems studied by most cell biologists. They include:
eukaryotes. All share the ability to colonize their hosts and cause the cytoskeleton, organelles and membrane-trafficking intermedi-
pathology through their interactions with host cells. ates, signal transduction pathways, cell cycle regulators, the organ-
To influence host cells, each pathogen produces a distinct set of elle and protein recycling machinery, and cell-death pathways
virulence factors that target specific host cell structures, pathways, (Table 1). Studying the mechanisms by which virulence factors target
and molecules. The function of virulence factors differs depending host cells has two important impacts. First, such studies reveal cru-
on where the pathogen establishes residence (Figure 1). Extracellu- cial mechanisms of infection. Second, these studies aid in the eluci-
lar pathogens reside around or in contact with host cells but resist dation of fundamental cellular mechanisms—for example, tyrosine
internalization into cells. They produce virulence factors that inhibit kinase signaling or actin-based motility, to name a very few.
phagocytosis and otherwise disable elements of the immune re- The study of pathogen interactions with host cells also has practi-
sponse. Intracellular pathogens instead encourage their internaliza- cal impacts on fighting infectious diseases. One is advancing our
tion into host cells, grow within a preferred cellular compartment or understanding of immunity. Immune cells are often the targets of
pathogen virulence factors, and understanding the interactions of
pathogens with immune cells enhances the development of effec-
tive immune-based therapies for infections. Another is identifying
DOI:10.1091/mbc.E15-03-0144 cellular molecules crucial for infection, which are then exploited as
Address correspondence to: Matthew D. Welch (welch@berkeley.edu). targets of drugs to treat infectious diseases.
Abbreviations used: A-MuLV, Abelson murine leukemia virus; BCG, bacillus
Calmette-Guerin; RSV, Rous sarcoma virus; SCV, Salmonella-containing vacuole. In this Perspective, I provide concrete answers to the basic ques-
© 2015 Welch. This article is distributed by The American Society for Cell Biology tion posed in the title: Why should cell biologists study microbial
under license from the author(s). Two months after publication it is available to pathogens? Along the way, I explore three smaller questions: What
the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Cre-
ative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).
have we learned about basic cell biology from studying pathogens
“ASCB®,” “The American Society for Cell Biology®,” and “Molecular Biology of and their virulence factors? What has studying the cell biology of
the Cell®” are registered trademarks of The American Society for Cell Biology. host–pathogen interactions taught us about immunity? How has

Volume 26  December 1, 2015 4295 


extracellular pathogens intracellular pathogens inhibit phagocytosis by producing virulence
factors that disable Rho, Rac, and/or Cdc42,
Clostridium species, others Trypanosoma cruzi
highlighting the generality of this patho-
genic strategy (Lemichez and Aktories,
inhibit promote 2013). Bacterial toxins continue to be im-
phagocytosis phagocytosis
portant tools for revealing the functions of
Rho GTPases in cells.
Rho GTPases lysosome The study of pathogens that mobilize ac-
disable Ca 2+
actin manipulate tin for movement has also led to the discov-
secretion
autophagy ery of fundamental mechanisms of cytoskel-
septins Salmonella, Legionella etal dynamics and regulation. Such
nucleus p62, NDP52 pathogens include the bacteria Listeria
SNAREs
monocytogenes, Shigella flexneri, and
DNA tumor Listeria, Shigella alter Escherichia coli, which cause food-borne ill-
viruses Rab, Arf trafficking nesses, as well as vaccinia virus, which is the
smallpox vaccine strain. These microbes un-
alter dergo actin-based motility either within or
cell cycle caspase-1 on the surface of cells, which enables cell-
pRb, Cdks, inflammasomes to-cell spread during infection (Welch and
cyclins Arp2/3, actin p53, Bcl-2 Way, 2013). Through biochemical reconsti-
promote movement influence cell death tution of L. monocytogenes and/or S. flex-
neri motility, the host Arp2/3 complex and
its activators (the WASP family proteins)
FIGURE 1:  Pathogen virulence factors influence cellular pathways and structures. Extracellular were revealed as key actin-nucleating fac-
pathogens produce virulence factors that act at a distance or on contact with a host cell. These tors for bacterial pathogens and host cells
virulence factors inhibit cellular processes (indicated by red) including phagocytosis and (Welch et al., 1997, 1998), and a minimal set
secretion. In contrast, intracellular pathogens produce virulence factors that promote intimate of proteins that is sufficient to drive actin-
interactions with host cells. These activate cellular processes (indicated by green), including
based motility was defined (Loisel et al.,
phagocytosis, intracellular movement to a preferred compartment or organelle, and cell-to-cell
1999). Moreover, the study of enteropatho-
spread. Virulence factors can also either activate or inactivate cellular processes (indicated by
orange) to prevent microbial killing and enable growth and replication. These pathways include genic/enterohemorrhagic E. coli and vac-
those involved in membrane trafficking, autophagy, cell death, and cell cycle regulation. cinia virus, which induce actin assembly
from outside the cell through the plasma
membrane, revealed important roles for ty-
identifying cellular targets of pathogens led to the development of rosine kinase signaling and protein clustering in regulating actin as-
therapeutic agents to treat infection? sembly (Frischknecht et al., 1999; Campellone et al., 2008).
Studying pathogens has also led to fundamental advances in the
WHAT HAVE WE LEARNED ABOUT BASIC CELL BIOLOGY field of membrane trafficking. A classic example involves the extra-
FROM STUDYING PATHOGENS AND THEIR VIRULENCE cellular bacterial pathogens C. botulinum, mentioned above, as well
FACTORS? as Clostridium tetani, which causes the paralytic disease tetanus. In
The study of how pathogens and their virulence factors impact host addition to the C3 exoenzyme, C. botulinum produces botulinum
cells has been fertile ground for uncovering basic cell biological toxins A–G (type A is familiarly known as Botox), and C. tetani se-
principles and mechanisms. Such discoveries have enhanced our cretes tetanus toxin. These toxins specifically cleave SNARE protein
understanding of the many structures, pathways, and molecules components of the vesicle fusion machinery, including VAMP, SNAP-
that are commonly exploited by pathogens during infection. 25, and syntaxin (Link et al., 1992; Schiavo et al., 1992; Blasi et al.,
One area of cell biology in which the study of pathogens has 1993a,b). Microinjection of nerve cells with these toxins showed that
enabled fundamental advances is the cytoskeletal field. Extracellular SNARE molecules are critical for neurotransmitter release via vesicle
bacterial pathogens often target actin or its regulators by secreting fusion with the plasma membrane (Schiavo et al., 1992; Blasi et al.,
toxins that translocate across cellular membranes to inhibit phago- 1993b). Preventing neurotransmitter release results in the paralysis
cytosis by immune cells (Lemichez and Aktories, 2013). An example caused by botulinum and tetanus toxins. In a contemporary study, it
is Clostridium botulinum, which causes the paralytic illness botulism. was revealed that SNARE proteins form a complex that is sufficient
C. botulinum produces several secreted toxins, including C3 toxin, to mediate vesicle docking and fusion (Söllner et al., 1993). Thus
which enters host cells and ADP-ribosylates and inactivates the Rho bacterial toxins were used in discovering fundamental mechanisms
family GTPase Rho (paralysis is caused by a separate toxin, as dis- of membrane fusion and vesicular transport.
cussed below; Narumiya et al., 1988; Aktories et al., 1989). By exam- Advances in our understanding of how membrane-trafficking
ining the effect of microinjecting C3 toxin into cells, Alan Hall and pathways contribute to repairing plasma membrane wounds
coworkers discovered that Rho signals to promote the formation of (Sonnemann and Bement, 2011) have also come from the study of
focal adhesions and stress fibers (Chardin et al., 1989; Paterson intracellular pathogens. A classic example is Trypanosoma cruzi, a
et al., 1990; Ridley and Hall, 1992). Sadly, Alan passed away earlier eukaryotic parasite and the causative agent of Chagas disease,
this year in the prime of his career. Similar studies showed that Rho which in its chronic form can cause cardiovascular and intestinal ill-
family proteins are also required for phagocytosis (Hall, 2012). Many ness. As the T. cruzi parasite contacts the plasma membrane of a
bacteria, such as Clostridium difficile, the leading cause of hospital- host cell before invasion, intracellular Ca2+ is elevated, and cellular
acquired diarrhea, or Yersinia pestis, the causative agent of plague, lysosomes are recruited to the point of contact between the parasite

4296 | M. D. Welch Molecular Biology of the Cell


Pathway/structure Pathogenic process Pathogens Host targets References
Cytoskeleton Inhibit phagocytosis Many extracellular pathogens, e.g., Rho proteins, actin Lemichez and
Clostridium spp., Yersinia spp. Aktories, 2013
Phagocytosis Most intracellular pathogens Rho proteins, signaling Pizarro-Cerdá and
proteins, phagocytic Cossart, 2006
proteins, actin
Movement, spread Many pathogens, e.g., L. monocy- Arp2/3 complex, Welch and Way,
togenes, S. flexneri, E. coli, vaccinia signaling proteins, 2013
virus actin
Membrane Growth/replication Many extracellular pathogens, e.g., C. SNARE proteins, Rab Asrat et al., 2014
trafficking botulinum, C. tetani; many intracel- proteins, Arf proteins
lular pathogens, e.g., T. cruzi, L. pneu-
mophila
Cell cycle Growth/replication Many viruses, e.g., adenovirus, human pRb, cyclins, Cdks Bagga and
papilloma virus, SV40 Bouchard, 2014
Signal transduction Growth/replication Many pathogens, e.g., vaccinia virus, Tyrosine kinases, other Martin, 2004
RSV, A-MuLV kinases, GTPases, lipid
modifiers
Autophagy Growth/replication Many intracellular pathogens, e.g., S. NDP52, p62, optineurin Mostowy, 2014;
Typhimurium, L. monocytogenes, S. Sorbara and
flexneri, M. tuberculosis Girardin, 2015
Cell death Growth/replication Many pathogens, e.g., S. Caspase-1, inflamma- Guo et al., 2015
Typhimurium, P. falciparum somes, p53, Bcl-2
This table is meant to provide important and interesting examples without being comprehensive.

TABLE 1:  Summary of cellular pathways targeted by pathogens.

and host cell. Surprisingly, lysosomes participate in exocytosis at the influenced by the study of viruses (Martin, 2004). Famous examples
invasion site, which facilitates invasion (Tardieux et al., 1992, 1994). are the Rous sarcoma virus (RSV), which causes sarcomas in chick-
It was later revealed that the Ca2+-dependent fusion of lysosomes ens, and Abelson murine leukemia virus (A-MuLV), which causes
(Reddy et al., 2001) and other organelles (Shen et al., 2005) plays a lymphosarcomas in mice. The capacity of RSV to transform normal
key role in repairing plasma membrane wounds in uninfected cells. cells into tumor cells was found to be associated with the viral src
Along with work on T. cruzi, studying how intracellular bacterial gene and its product v-Src (Brugge and Erikson, 1977; Weiss et al.,
pathogens such as Legionella pneumophila, the causative agent of 1977). The v-Src protein and the v-Abl protein from A-MuLV were
Legionnaire’s disease, manipulate membrane-trafficking pathways is subsequently shown to be tyrosine kinases (Hunter and Sefton,
advancing our understanding of these pathways in uninfected cells 1980; Witte et al., 1980), the first discovery of this protein class. Cel-
(Asrat et al., 2014). lular homologues of these proteins, c-Src and c-Abl, were soon
Cell cycle regulatory mechanisms have also been exposed identified (Stehelin et al., 1976; Shalloway et al., 1981; Heisterkamp
through the investigation of virus interactions with host cells (Bagga et al., 1982), demonstrating that viral oncogenes are derived from
and Bouchard, 2014). Classic examples involve the study of DNA cellular counterparts. It was also soon recognized that the human
tumor viruses, which include adenovirus, human papilloma virus, and ABL1 gene, which encodes c-Abl, participates in the Philadelphia
SV40. These viruses rely on the host DNA replication machinery, and chromosomal translocation, which is commonly associated with leu-
thus they induce cell cycle progression into S phase to favor viral kemias (de Klein et al., 1982). Thus viruses were key to demonstrat-
DNA replication. A key discovery was that these viruses encode pro- ing the importance of tyrosine kinases in signaling in normal and
teins, such as E1A from adenovirus, that bind to the tumor-suppres- cancer cells and the roles of oncogenes in cancer. Future studies of
sor protein pRb and related proteins (Whyte et al., 1988). The role of pathogens will continue to reveal ways in which diverse signaling
pRb as a negative regulator of cell cycle progression was subse- pathways and proteins influence normal cell physiology and
quently revealed when it was found that E1A binding to pRb com- disease.
petes with and releases the bound transcription factor E2F, which
turn activates the expression of cell cycle regulatory genes that pro- WHAT CAN STUDYING THE CELL BIOLOGY OF
mote entry into S phase (Bagchi et al., 1991; Bandara and La HOST–PATHOGEN INTERACTIONS TEACH US ABOUT
Thangue, 1991; Chellappan et al., 1991; Raychaudhuri et al., 1991). IMMUNITY?
Other viruses target different cell cycle regulators, including Cdks Cells of the immune system are often targeted by pathogens to
and cyclins (Bagga and Bouchard, 2014), and studying how viruses avoid or subvert immune defenses. Certain facets of the interaction
manipulate host cells will continue to reveal cell cycle regulatory between pathogens and immune cells lie at the interface between
mechanisms. the fields of immunology and cell biology. The study of such areas is
Finally, our understanding of signal transduction pathways and of increasing importance in understanding general mechanisms of
their contribution to diseases like cancer has also been heavily pathogenesis, and may prove particularly relevant in harnessing the

Volume 26  December 1, 2015 Cell biology of pathogenesis | 4297 


immune system to fight infection. In this section, I highlight emerging pacted DNA fragmentation, and loss rather than maintenance of
areas of intersection between basic cellular pathways and the innate plasma membrane integrity (Brennan and Cookson, 2000). This
immune response to pathogens. In the subsequent section, I dis- mechanism of cell death was subsequently called pyroptosis, which
cuss how studying these areas impacts the development of thera- is a proinflammatory cell death, to distinguish it from apoptosis,
peutics to treat infectious diseases. which is anti-inflammatory. Subsequent studies showed that cas-
Autophagy has emerged as a process that is of central inter- pase-1 activation involves a multiprotein complex called an inflam-
est in the fields of cell biology and immunology, and research in masome (Martinon et al., 2002), of which there are multiple variet-
both disciplines has synergized to reveal key ways in which au- ies with different functions in innate immunity and inflammation
tophagy impacts basic cell function and disease. Studies by cell (Guo et al., 2015). In addition to their roles in infection, inflamma-
biologists have uncovered the importance of autophagy in main- somes also play an important role in metabolic and neurological
taining homeostasis during normal, stressful, or disease condi- diseases (Guo et al., 2015). The continued study of inflammasomes
tions, and have identified important molecular players in this will enhance our understanding of inflammatory responses to infec-
pathway (Boya et al., 2013). Immunologists have discovered that tion and of the role of inflammation in normal cell function and
autophagy of pathogens (also called xenophagy) is an important disease.
arm of the innate immune response that promotes intracellular
pathogen sequestration in autophagosomes and their degrada- HOW HAS IDENTIFYING CELLULAR TARGETS OF
tion in lysosomes (Huang and Brumell, 2014; Sorbara and PATHOGENS LED TO THE DEVELOPMENT OF
Girardin, 2015). THERAPEUTIC AGENTS TO TREAT INFECTION?
An example of how studying pathogens has advanced our under- There are two predominant approaches for combating infectious
standing of autophagy mechanisms involves the response to infec- diseases. One is to stimulate the immune system to prevent or re-
tion by the intracellular pathogen Salmonella enterica serovar Ty- duce the impact of infection, for example, through vaccination. An-
phimurium (S. Typhimurium), a common cause of diarrheal illness. S. other is to reduce or eliminate an existing infection with drugs that
Typhimurium normally resides within an endosome-like compartment kill the infectious agent and/or enhance the immune response.
called the Salmonella-containing vacuole (SCV). However, observa- Studying the cell biology of pathogenesis is contributing to both of
tion of the bacteria that occasionally damage the SCV and escape these therapeutic avenues.
into the cytosol enabled the discovery of previously unknown mecha- An interesting example involves an emerging connection be-
nisms by which pathogens are targeted to autophagy. These include tween autophagy and vaccine efficacy. The bacillus Calmette-
marking bacteria in the cytosol with ubiquitin (Thurston et al., 2009) Guerin (BCG) vaccine, used to combat tuberculosis caused by the
and marking those in damaged SCVs with the lectin galectin-8, which intracellular pathogen Mycobacterium tuberculosis, consists of an
recognizes glycans on damaged vacuoles (Thurston et al., 2012). attenuated strain of the related bacterium Mycobacterium bovis.
Both galectin-8 and ubiquitin are then recognized by adapter pro- BCG has a protective effect against meningitis and disseminated
teins (including NDP52, p62, and optineurin), which recruit LC3 and tuberculosis in children but does not prevent primary infection with
initiate autophagosome formation (Thurston et al., 2009, 2012; M. tuberculosis or reactivation of pulmonary infection, which is the
Zheng et al., 2009; Wild et al., 2011). In addition to their roles in infec- main route of spread of the disease. Thus a more effective vaccine
tion, these same pathways may be involved in targeting damaged is needed. Interestingly, augmenting autophagy with rapamycin
organelles in uninfected cells (Huang and Brumell, 2014; Sorbara and was found to enhance presentation of a BCG antigen by antigen-
Girardin, 2015) and in removing protein aggregates, for example, presenting cells and enhance protection against M. tuberculosis
those associated with neurodegenerative diseases (Rubinsztein et al., infection in animal model (Jagannath et al., 2009). A similar phe-
2015). nomenon was observed for the yellow fever vaccine YF-17D, a live
A second example highlights how the study of pathogens can attenuated virus that, in contrast with BCG, is almost always effec-
reveal new pathways that influence autophagy, such as an emerging tive in protecting against infection with the yellow fever virus. It was
link between cytoskeletal elements and the autophagy machinery shown that YF-17D stimulated expression of the kinase GCN2,
(Mostowy, 2014). In the case of L. monocytogenes, the ability of the which in turn stimulated dendritic cells to initiate autophagy and
bacterial ActA protein to recruit actin-polymerizing factors masks enhanced antigen presentation to T-cells (Ravindran et al., 2014).
the bacteria from ubiquitination and the initiation of autophago- These findings suggest that stimulating autophagy may be a gen-
some formation (Yoshikawa et al., 2009). This suggests a potential eral strategy for enhancing antigen presentation and vaccine
role for actin in autophagy inhibition. In contrast, for S. flexneri, re- efficacy.
cruitment of actin promotes the subsequent recruitment of septin In cases in which vaccination is not possible or fails to confer
proteins, which cage the bacteria and are crucial for autophagy protection, antiviral, antibacterial, and antiparasitic drugs are com-
(Mostowy et al., 2010, 2011). Thus, in the case of S. flexneri, actin monly used to treat infections. These drugs generally target
and septins play a stimulatory role in autophagy. Deciphering the pathogen molecules that are both essential for pathogen growth
roles of cytoskeletal elements in autophagy regulation and the in- and are distinct from host molecules, enhancing the selective tox-
nate immune response should be an active area of future icity of the drug for the infectious agent while minimizing side ef-
investigation. fects on the host. This raises the following question: Can host cell
Beyond autophagy, the study of pathogens has revealed previ- components that are important for pathogenesis also be effective
ously unappreciated pathways for regulating programmed cell drug targets for treating infectious diseases? The answer is yes,
death that are integral to innate immunity and inflammation. One and it is noteworthy that targeting host molecules appears to be
such pathway was discovered by studying cell death induced by S. an emerging strategy for the development of drugs to treat
Typhimurium. It was noted that S. Typhimurium infection induced infections.
cell death in macrophages that was dependent on caspase-1 (Hersh Targeting host molecules has advanced the furthest in develop-
et al., 1999). Moreover, the characteristics of death were distinct ing treatments for viral infections. Prime examples are drugs that
from apoptosis in key respects, including diffuse rather than com- target host cell receptor molecules and prevent viral entry. Maraviroc

4298 | M. D. Welch Molecular Biology of the Cell


is a Federal Drug Administration (FDA)-approved drug that is used CONCLUSIONS AND FUTURE DIRECTIONS
in combination therapy to treat HIV infection. It inhibits viral entry In writing this Perspective, I hope to encourage cell biologists to
into cells by binding to the chemokine- and HIV-receptor CCR5 study pathogens by collaborating with pathogenesis researchers or
(Wood and Armour, 2005). Other inhibitors of host proteins in- incorporating work on infectious diseases into their own research
volved in HIV infection are also in development (Arhel and Kirch- programs. Such investigations might focus on well-known patho-
hoff, 2010). Moreover, inhibitors of the cellular receptors for other gens or new and emerging infectious agents. The motivation may
viruses have been identified. A small molecule that inhibits cellular be a desire to reveal new biological principles or to better understand
infection with Ebola virus, the causative agent of a dramatic hemor- and treat important diseases. Regardless of the choice of pathogen
rhagic fever, works by binding to the endosomal protein NPC1 or source of motivation, future studies by cell biologists will uncover
(Côté et al., 2011). In fact, the identification of this inhibitor revealed new ways in which pathogens influence host cell pathways and
that NPC1 is a crucial factor for Ebola virus infection. A more recent structures, and new cell biological mechanisms that operate under
study identified an engineered protein that inhibits infection with normal circumstances and in various disease states. Future studies
the influenza virus, which causes flu, by binding to sialic acid, which will also contribute to the development of new vaccines and drugs
is used as a receptor for virus entry (Connaris et al., 2014). One in- that target host cell proteins to prevent or treat infections. Therefore
tranasal dose of this inhibitor protected mice from an otherwise le- basic and translational research at the interface between microbiol-
thal dose of the 2009 pandemic H1N1 virus, while also enabling ogy, cell biology, and immunology will be an increasingly important
sufficient viral replication to potentially protect the animals from fu- source of information and innovation relevant to biology in general
ture infection. and infectious disease in particular.
Antibacterial agents that target host cell molecules are also be-
ing explored. Such agents will be particularly useful in cases for
ACKNOWLEDGMENTS
which there is no effective vaccine, and/or resistance to conven-
I thank Rebecca Lamason and Chris Patane for helpful comments on
tional antibiotics is common, as with M. tuberculosis. A recent fruit-
the manuscript. Work in the Welch lab is funded by National Insti-
ful approach was to screen through a library of bioactive small mol-
tutes of Health grants R01 GM059609 and R01 AI109044.
ecules known to target host proteins for those that restrict the
growth of M. tuberculosis (Stanley et al., 2014). This identified
compounds that affect several protein classes, including G pro- REFERENCES
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Volume 26  December 1, 2015 Cell biology of pathogenesis | 4301 

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